aboutsummaryrefslogtreecommitdiff
path: root/biology/py-biopython
diff options
context:
space:
mode:
authorJohann Visagie <wjv@FreeBSD.org>2001-09-06 12:42:36 +0000
committerJohann Visagie <wjv@FreeBSD.org>2001-09-06 12:42:36 +0000
commit5f3039ab6076092726b854406105df809b1635ad (patch)
tree759bb416619015aa2d4bb3c3b977f0d150ccfb24 /biology/py-biopython
parenta2fc4e6d3207ccdf2ffbfa55f969e76ab2e055ac (diff)
downloadports-5f3039ab6076092726b854406105df809b1635ad.tar.gz
ports-5f3039ab6076092726b854406105df809b1635ad.zip
Notes
Diffstat (limited to 'biology/py-biopython')
-rw-r--r--biology/py-biopython/Makefile41
-rw-r--r--biology/py-biopython/distinfo2
-rw-r--r--biology/py-biopython/pkg-plist212
-rw-r--r--biology/py-biopython/pkg-req17
4 files changed, 167 insertions, 105 deletions
diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index e59a64a4cae6..2787d9a959ea 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -6,7 +6,7 @@
#
PORTNAME= biopython
-PORTVERSION= 1.00.a2
+PORTVERSION= 1.00.a3
CATEGORIES= biology python
MASTER_SITES= http://www.biopython.org/Download/
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -17,16 +17,14 @@ MAINTAINER= wjv@FreeBSD.org
BUILD_DEPENDS= ${PYDISTUTILS}
RUN_DEPENDS= ${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-martel \
- ${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/py-numeric
-
-# Biopython requires Python 2.0 or above:
-PYTHON_VERSION= python2.1
+ ${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/py-numeric \
+ ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
+USE_PYTHON= yes
PLIST_SUB+= PLIST_CORBA=${PLIST_CORBA} PLIST_OMNIORB=${PLIST_OMNIORB} \
PLIST_FNORB=${PLIST_FNORB}
CPIO= cpio --quiet -pdum -R
-DOCDIR= ${PREFIX}/share/doc/py-biopython
-EGDIR= ${PREFIX}/share/examples/py-biopython
+EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME}
# CORBA support (a.k.a Biopython-CORBA):
# Set WITH_CORBA to enable CORBA support for the Biopython port.
@@ -41,7 +39,7 @@ EGDIR= ${PREFIX}/share/examples/py-biopython
# - ORBit is a very popular and elegant ORB. The ORBit-Python bindings are
# used.
# Since Fnorb is distributed under a non-free licence and ORBit support in
-# Biopython-CORBA is not yet stable, "omniorb" is the default.
+# Biopython-CORBA is reputedly not yet stable, "omniorb" is the default.
CORBA_ORB?= omniorb
CORBA_VERSION= 0.2.1
@@ -57,6 +55,7 @@ PLIST_OMNIORB= ""
PLIST_FNORB= "@comment "
.elif ${CORBA_ORB} == "fnorb"
BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
+RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
CORBA_ORBNAME= Fnorb
EXTRA_PATCHES+= ${PATCHDIR}/extra-patch-build_helper.py
PLIST_OMNIORB= "@comment "
@@ -92,6 +91,9 @@ do-build:
@ cd ${CORBA_WRKSRC} && ${PYTHON_CMD} setup.py build
.endif
+pre-install:
+ @ ${SH} ${PKGREQ} INSTALL
+
do-install:
@ cd ${WRKSRC} && ${PYTHON_CMD} setup.py install -c -O1 \
--prefix=${PREFIX}
@@ -102,24 +104,25 @@ do-install:
post-install:
.if !defined(NOPORTDOCS)
- @ ${MKDIR} ${DOCDIR}
+ @ ${MKDIR} ${DOCSDIR}
.for docfiles in *.txt *.tex *.py
- @ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCDIR}
+ @ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCSDIR}
.endfor
- @ ${MKDIR} ${EGDIR}
- @ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EGDIR}
+ @ ${MKDIR} ${EXAMPLESDIR}
+ @ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EXAMPLESDIR}
@ cd ${WRKSRC} && find Scripts \
- | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR}
+ | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
.if defined(WITH_CORBA)
- @ ${MKDIR} ${DOCDIR}/BioCorba
+ @ ${MKDIR} ${DOCSDIR}/BioCorba
.for docfiles in *.tex *.pdf
- @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCDIR}/BioCorba
+ @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCSDIR}/BioCorba
.endfor
- @ ${MKDIR} ${EGDIR}/BioCorba
+ @ ${MKDIR} ${EXAMPLESDIR}/BioCorba
@ cd ${CORBA_WRKSRC}/Doc/examples && find * \
- | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR}/BioCorba
- @ ${MKDIR} ${EGDIR}/BioCorba/Scripts
- @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* ${EGDIR}/BioCorba/Scripts
+ | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}/BioCorba
+ @ ${MKDIR} ${EXAMPLESDIR}/BioCorba/Scripts
+ @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* \
+ ${EXAMPLESDIR}/BioCorba/Scripts
.endif # defined(WITH_CORBA)
.endif # !defined(NOPORTDOCS)
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index 5627a525c266..d88599879874 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,2 +1,2 @@
-MD5 (biopython-1.00a2.tar.gz) = 416fb1ab08dfdd7f3d4d75bc0043ace8
+MD5 (biopython-1.00a3.tar.gz) = be59a12eeb2c0bcdd82a73dfd7bcc615
MD5 (biopython-corba-0.2.1.tar.gz) = 3d6d3e4570ff2996bef84e08f6fabc25
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index a7b709a312f1..8a4749f0eb0b 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -201,73 +201,74 @@
%%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.py
%%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.pyc
%%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.pyo
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/IntroPythonClient.pdf
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/IntroPythonClient.tex
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/README.pdf
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/README.tex
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/biocorbahowto.pdf
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/biocorbahowto.tex
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/secret_message_client.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/secret_message_idl.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/biosequence_client.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/biosequence_idl.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers__POA/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_client.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_idl.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/Scripts/bioenv_server.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/a_drought.fasta
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/a_drought.gb
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/embl_biocorba.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_bioenv.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_biopy.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_pseqit.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_server.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gb_bioenv.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gbclient.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gbsrv.pl
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/genbank_db_server.py
-%%PORTDOCS%%share/doc/py-biopython/Blast.txt
-%%PORTDOCS%%share/doc/py-biopython/Enzyme.txt
-%%PORTDOCS%%share/doc/py-biopython/Fasta.txt
-%%PORTDOCS%%share/doc/py-biopython/Medline.txt
-%%PORTDOCS%%share/doc/py-biopython/Parser.txt
-%%PORTDOCS%%share/doc/py-biopython/Prosite.txt
-%%PORTDOCS%%share/doc/py-biopython/References.txt
-%%PORTDOCS%%share/doc/py-biopython/SCOP.txt
-%%PORTDOCS%%share/doc/py-biopython/SwissProt.txt
-%%PORTDOCS%%share/doc/py-biopython/Tutorial.tex
-%%PORTDOCS%%share/doc/py-biopython/Tutorial.txt
-%%PORTDOCS%%share/doc/py-biopython/make_api_docs.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/SeqGui/SeqGui.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/query_pubmed.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/README
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/nextorf.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/test.fas
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/testrp.fas
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_blast.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_blastbg.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_io.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_sequence.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_translations.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_utils.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_widget.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbbtools.py
-%%PORTDOCS%%share/examples/py-biopython/clustal_run.py
-%%PORTDOCS%%share/examples/py-biopython/fasta_consumer.py
-%%PORTDOCS%%share/examples/py-biopython/fasta_dictionary.py
-%%PORTDOCS%%share/examples/py-biopython/fasta_iterator.py
-%%PORTDOCS%%share/examples/py-biopython/getgene.py
-%%PORTDOCS%%share/examples/py-biopython/local_blast.py
-%%PORTDOCS%%share/examples/py-biopython/make_subsmat.py
-%%PORTDOCS%%share/examples/py-biopython/pubmed_search.py
-%%PORTDOCS%%share/examples/py-biopython/query_entrez.py
-%%PORTDOCS%%share/examples/py-biopython/swissprot.py
-%%PORTDOCS%%share/examples/py-biopython/www_blast.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/IntroPythonClient.pdf
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/IntroPythonClient.tex
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/README.pdf
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/README.tex
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/biocorbahowto.pdf
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/biocorbahowto.tex
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/secret_message_client.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/secret_message_idl.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/biosequence_client.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/biosequence_idl.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers__POA/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_client.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_idl.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/Scripts/bioenv_server.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/a_drought.fasta
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/a_drought.gb
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/embl_biocorba.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_bioenv.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_biopy.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_pseqit.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_server.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gb_bioenv.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbclient.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbsrv.pl
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/genbank_db_server.py
+%%PORTDOCS%%share/doc/biopython/Blast.txt
+%%PORTDOCS%%share/doc/biopython/Enzyme.txt
+%%PORTDOCS%%share/doc/biopython/Fasta.txt
+%%PORTDOCS%%share/doc/biopython/KEGG.txt
+%%PORTDOCS%%share/doc/biopython/Medline.txt
+%%PORTDOCS%%share/doc/biopython/Parser.txt
+%%PORTDOCS%%share/doc/biopython/Prosite.txt
+%%PORTDOCS%%share/doc/biopython/References.txt
+%%PORTDOCS%%share/doc/biopython/SCOP.txt
+%%PORTDOCS%%share/doc/biopython/SwissProt.txt
+%%PORTDOCS%%share/doc/biopython/Tutorial.tex
+%%PORTDOCS%%share/doc/biopython/Tutorial.txt
+%%PORTDOCS%%share/doc/biopython/make_api_docs.py
+%%PORTDOCS%%share/examples/biopython/Scripts/SeqGui/SeqGui.py
+%%PORTDOCS%%share/examples/biopython/Scripts/query_pubmed.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/README
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/nextorf.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/test.fas
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/testrp.fas
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blast.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blastbg.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_io.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_sequence.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_translations.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_utils.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_widget.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbbtools.py
+%%PORTDOCS%%share/examples/biopython/clustal_run.py
+%%PORTDOCS%%share/examples/biopython/fasta_consumer.py
+%%PORTDOCS%%share/examples/biopython/fasta_dictionary.py
+%%PORTDOCS%%share/examples/biopython/fasta_iterator.py
+%%PORTDOCS%%share/examples/biopython/getgene.py
+%%PORTDOCS%%share/examples/biopython/local_blast.py
+%%PORTDOCS%%share/examples/biopython/make_subsmat.py
+%%PORTDOCS%%share/examples/biopython/pubmed_search.py
+%%PORTDOCS%%share/examples/biopython/query_entrez.py
+%%PORTDOCS%%share/examples/biopython/swissprot.py
+%%PORTDOCS%%share/examples/biopython/www_blast.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyo
@@ -280,6 +281,15 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/Generic.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.pyo
@@ -358,6 +368,24 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase/__init__.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyo
@@ -445,6 +473,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/SProt.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.pyo
@@ -464,6 +495,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/__init__.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyo
@@ -521,6 +555,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/__init__.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.pyo
lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.py
lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyc
lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
@@ -540,6 +577,10 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/PDB
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta
@@ -552,24 +593,24 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Align
@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/Scripts
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/py-biopython/BioCorba
-%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts/xbbtools
-%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts/SeqGui
-%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts
-%%PORTDOCS%%@dirrm share/examples/py-biopython
-%%PORTDOCS%%@dirrm share/doc/py-biopython
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/Scripts
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers__POA
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/biopython/BioCorba
+%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/xbbtools
+%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/SeqGui
+%%PORTDOCS%%@dirrm share/examples/biopython/Scripts
+%%PORTDOCS%%@dirrm share/examples/biopython
+%%PORTDOCS%%@dirrm share/doc/biopython
%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/ensembl_skel
%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel/seqcore_skel
%%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel
@@ -597,3 +638,4 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio
%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters
%%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba
+
diff --git a/biology/py-biopython/pkg-req b/biology/py-biopython/pkg-req
new file mode 100644
index 000000000000..481af4e9a7ad
--- /dev/null
+++ b/biology/py-biopython/pkg-req
@@ -0,0 +1,17 @@
+#!/bin/sh
+
+PATH=$PATH:/usr/local/bin
+
+if [ "x$1" = "xINSTALL" -o "x$2" = "xINSTALL" ]; then
+ PYTHON_GT=`python -c 'import string, sys; \
+ print string.split(sys.version)[0] >= "2.0"'`
+ if [ "x${PYTHON_GT}" = "x1" ]; then
+ exit 0
+ else
+ echo "-----------------------------------------------------------"
+ echo "Biopython requires Python version 2.0 or greater - "
+ echo " please update your Python installation before proceeding."
+ echo "-----------------------------------------------------------"
+ exit 1
+ fi
+fi